Andrew and Marit Miner's daily commute involves a leisurely 10-minute ride in a rowing boat, accompanied by schooling fish and occasional dolphins. Their home – a grass-thatched cottage powered by wind and solar energy – sits high on a limestone karst facing a blue-on-blue vista that stretches to a misty chain of atolls on the horizon. The nearest place with any infrastructure is Sorong, a dreary and dilapidated industrial port in West Papua, four hours away by speedboat.

Four years ago, Andrew decided that this far-flung marine frontier in the remote eastern waters of the Indonesian archipelago would make a great place for a resort. So he persuaded Marit to leave Bangkok, where she ran a clothing business, gave up his job as a guide on a dive boat, secured funding from 40 friends and acquaintances and built the Misool Eco Resort.

You could think them crazy to set up home and a business somewhere so remote, but this area – known as Raja Ampat, or Four Kings, after its major islands – is home to the greatest concentration of marine biodiversity on the planet, a fact scientists discovered only in the past decade. It took me and the photographer two days to get there from Bali, with an overnight stop in Makassar, capital of South Sulawesi province, and another night in Sorong (Raja Ampat regulars wryly pronounce it "so wrong"). The journey from the UK can be done in two days, too, with a stopover in Jakarta. And it is well worth the effort.

Andrew and Marit's DIY approach has produced a low-impact enclave that wouldn't look out of place in the Maldives. The wood – all 600 tonnes of it – used to build the year-old resort came from fallen trees. Biological waste is used to fertilise the gardens, creating a closed system and feeding plants such as lemon grass, ginger and heliconia. The whole aesthetic is by turns whimsical and quietly sophisticated, with weathered wooden walkways connecting nine water cottages, a restaurant pavilion and a dive centre, all fringing a shallow cove on the edge of the resort's house reef. There are crayons on the driftwood table by my bed and a view inspiring enough to make me use them.

Stingray, octopus, reef shark, bumphead parrotfish, barracuda – I spot all of these, and not on a dive but from the veranda of my cottage – a cosy little thatched folly with a cushion-strewn bed under a diaphanous mosquito net and a bathroom open to the sky. Diving aside, this would make a great place for a honeymoon.

Under the water lurk stranger beings – elaborately armoured scorpion fish, weird patterned carpet sharks, neon nudibranchs with wispy rainbow filaments and pygmy seahorses, which barely reach an inch in length. The scale, density and variety of the coral are unlike anything I've ever seen. Scientists estimate that 75% of the earth's reef-building corals can be found in Raja Ampat, and new marine species are being discovered, seemingly every other week.

Things are just as interesting above the water. One afternoon, we wend our way by boat through the limpid channels of a marine lagoon studded with jungle-drenched islets. On one of these rocky outposts we see 5,000-year-old petroglyphs depicting dolphins, handprints and other nameless symbols.

"Nowhere else I know has such spectacularly beautiful scenery both above and below water," says Andrew. "It's the combination that's so special – reefs to rainforests. And we have this 425-square-mile Marine Protected Area (MPA) at the very centre of the greatest concentration of marine biodiversity on the planet – that's huge."

Andrew came to south-east Asia 17 years ago to escape the winter doldrums of his native Cornwall, became a dive master and took to the endlessly varied waters of the Malay archipelago on board a converted phinisi sailing boat. These elegant wooden liveaboards, built by the seafaring Bugis people of Sulawesi, are popular with divers. Over the course of seven years, he witnessed reefs and marine life diminishing everywhere, through a mix of destructive fishing and unregulated tourism. Then he came to Raja Ampat.

"It might sound dramatic, but this place is of global importance," Andrew says as we take afternoon tea on the veranda of the circular restaurant pavilion, a daily ritual here. Three baby reef sharks glide back and forth a few feet away, a surreal counterpoint to my Earl Grey and shortbread. "Scientists reckon that coral species here may be more resistant to [stress-induced] bleaching. We're also part of the Indonesian through-flow, which carries coral spawn and larvae down into the rest of Indonesia, restocking many of its reefs."

When I remark on the profusion of baby sharks on their doorstep, Andrew and Marit exchange meaningful smiles. "This place used to be a shark-finning camp," says Marit, a Swedish-American with a flair for good design (she handled the interiors) and smart marketing. "You only see babies because the adult population was almost destroyed [by the practice of harvesting shark fins and dumping the rest of the carcass at sea]. They're coming back, but it will take a decade for things to stabilise again."

The change of use is encouraging, all the more so because local people have a vested interest in conservation. A no-fishing zone means nothing unless you can enforce it, so having secured funding from campaigning group WildAid, Misool Eco Resort now has a boat crewed by local people running patrols four times a week and is lobbying to extend the no-take zone.

The next day, I find myself in the sparse, neatly kept home of Hadir Yelkom, an elder of Yellu village on Misool island itself, an hour's ride by speedboat from Misool Eco Resort. He welcomes the businesses that have moved in: "Before, we couldn't stop outsiders from fishing here illegally because we couldn't catch them in our long boats," he says, referring to the encroachment of big industrial boats from other parts of Indonesia and as far afield as the Philippines. "The local businesses gave us speedboats to chase them and now they don't come anymore." Having a bunch of fierce-looking Papuans confiscate your fishing gear before politely asking you to leave is clearly a strong deterrent.

A group of children peer in at us from the doorway; others are doing back flips off the jetty for the benefit of the photographer. It is afternoon, and most of the adults are at work in the nearby pearl farm, a relatively sustainable marine industry since oysters need optimal conditions to bear pearls – plus vigilant security.

For its part, Misool Eco Resort employs more than 60 people, many of them from Yellu. But the village does more than provide a workforce, it's also the leaseholder and proprietor of a vast tract of marine territory that not even the Indonesian government would dispute. The three NGOs working in the area, Conservation International, The Nature Conservancy and World Wildlife Fund have recognised the value of this clan-based system of ancestral tenure and are concentrating their efforts on making conservation goals dovetail with those of local people, using sustainable tourism as an economic incentive. Working closely with government and local communities, they've managed to establish seven Marine Protected Areas – the challenge now is to manage them effectively.

But the NGOs weren't the first people to engage with this place; rather a few intrepid pioneers who came for reasons other than conservation. After a week at Eco Misool Resort, I meet the man I'm told blazed Raja Ampat's watery trails.

A dugong is not something I ever imagined laying eyes upon, much less from the air. From an altitude of 250m, it is a pale silhouette against the blue, whale-shaped to my untrained eye. The pilot, Max Ammer, spotted it, even though he was busy keeping our two-seater ultralight aloft.

"This is absolutely the best way to patrol Raja Ampat," the Dutchman tells me over the intercom. As if to prove his point, we spot a ramshackle vessel in a concealed bay, leaking a slick of oil. We promptly dive to 20m to let the crew know they've been seen.

Max runs Papua Diving, run from two resorts on the island of Kri, close to Raja Ampat's biggest island, Waigeo. He first came out to Raja Ampat 20 years ago, in search of military hardware abandoned when the war in the Pacific ended abruptly with the atomic bomb. He sold vintage parts retrieved from jungles and underwater wrecks to collectors, made a tidy sum and diversified into dive tourism, building Sorido Bay, the area's only other luxury resort, a collection of seven bungalows and a first-floor lounge restaurant that resembles a traditional long house. His other project, Kri Eco Resort, a 10-minute walk round a headland, is more basic but visually captivating – six houses on stilts around a jetty, with a backdrop of electric-green rainforest. The diving here is as spectacular as at Misool, but different, with lots of hard corals and thick schools of big, pelagic fish.

Like Andrew and Marit, Max has close links with local communities and conservation groups. He employs around 100 staff, most of them Papuan, and is committed to investing in their training and education – many of his dive masters used to be fishermen. His dive manager, Otto Awom, a big, softly spoken man who regales me with local folktales one evening, has been his friend and collaborator for 16 years.

The plane was bought with a grant from Conservation International, with the proviso that Max conduct regular patrols looking for illegal boats and signs of destructive fishing practices. While he's largely positive about conservation efforts, he echoes a sense of urgency and frustration I also detected in Misool: "It's like having a ship with a leak and measuring how long it will take before it sinks. You have to fix the leak first." He believes more effort should be directed towards enforcing no-fishing zones and eradicating destructive fishing practices. "And then education, that's the most important thing in the long term," he adds.

Like so many hitherto-unexplored frontiers, Raja Ampat is emerging as a viable "destination". The resorts I stayed at had guests from the UK, Switzerland, the Netherlands and Germany as well as Asia – most, though not all of them, divers. The diving vanguard will soon be followed by other adventurers – both Misool Eco Resort and Papua Diving are planning to offer kayaking trips, and rock climbers will be drawn to the rugged monoliths that dot the islands. And I'm told the birdwatching is world-class. The challenge will be to develop tourism in tandem with conservation and community. These resorts are excellent examples of how that can work.

Way to go

Where to stay

Seven nights in a one-bedroom cottage at Misool Eco Resort costs from €1,490 per person, including transfers, all meals and one night with dinner en route in Sorong. A seven-night package at Kri Eco Resort with full board and four dives a day costs from €1,260 per person. A similar package at Sorido Bay costs from €1,791.

Getting there

Emirates flies to Jakarta from Gatwick from £471 return including taxes. Flights from Jakarta to Sorong cost about £100 with Express Air or Merpati. Boat transfers to Misool and Kri leave Sorong in the early afternoon.

Further information

All visitors to Raja Ampat must purchase a Rupiah 500,000 (£36) conservation fee. This can be done in Sorong at the JE Meridien hotel , or at the resorts.